Merge branch 'main' into dependabot/pip/lobsterpy-0.5.0

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.6.9
+  rev: v0.7.3
   hooks:
   - id: ruff
     args: [--fix]
@@ -17,7 +17,7 @@ repos:
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/asottile/blacken-docs
-  rev: 1.18.0
+  rev: 1.19.1
   hooks:
   - id: blacken-docs
     additional_dependencies: [black]
@@ -30,7 +30,7 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.11.2
+  rev: v1.13.0
   hooks:
   - id: mypy
     files: ^src/
@@ -41,11 +41,11 @@ repos:
   rev: v2.3.0
   hooks:
   - id: codespell
-    stages: [commit, commit-msg]
+    stages: [pre-commit, commit-msg]
     args: [--ignore-words-list, 'titel,statics,ba,nd,te,atomate']
     types_or: [python, rst, markdown]
 - repo: https://github.com/kynan/nbstripout
-  rev: 0.7.1
+  rev: 0.8.0
   hooks:
     - id: nbstripout
       args:

CHANGELOG.md

@@ -1,5 +1,32 @@
 # Change log
 
+## v0.0.18
+
+### New Features 🎉
+* Aims magnetic ordering by @tpurcell90 in https://github.com/materialsproject/atomate2/pull/922
+* Ferroelectric Workflow 2 by @fraricci in https://github.com/materialsproject/atomate2/pull/1012
+* Feat: GW workflow with VASP by @yanghan234 in https://github.com/materialsproject/atomate2/pull/808
+
+### Enhancements 🛠
+* Allow energy minimization maker to report energies by @orionarcher in https://github.com/materialsproject/atomate2/pull/1004
+* Implementation to adjust get_supercell_size to also generate orthorhombic supercells by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/923
+* MPMorph Flows by @BryantLi-BLI in https://github.com/materialsproject/atomate2/pull/938
+
+### House-Keeping 🧹
+* Fix `ruff` PLC0206 by @janosh in https://github.com/materialsproject/atomate2/pull/1009
+* Update MACE to 0.3.6 by @orionarcher in https://github.com/materialsproject/atomate2/pull/1032
+* Allow custom mace model by specifying "model" in calculator kwargs" by @orionarcher in https://github.com/materialsproject/atomate2/pull/1017
+* feat: add dedicated fireworks optional dependency (Fix #1033). by @hongyi-zhao in https://github.com/materialsproject/atomate2/pull/1035
+* Make testing utils importable by @jmmshn in https://github.com/materialsproject/atomate2/pull/1037
+
+### New Contributors
+* @fraricci made their first contribution in https://github.com/materialsproject/atomate2/pull/1012
+* @hongyi-zhao made their first contribution in https://github.com/materialsproject/atomate2/pull/1035
+* @BryantLi-BLI made their first contribution in https://github.com/materialsproject/atomate2/pull/938
+* @yanghan234 made their first contribution in https://github.com/materialsproject/atomate2/pull/808
+
+**Full Changelog**: https://github.com/materialsproject/atomate2/compare/v0.0.17...v0.0.18
+
 ## v0.0.17
 
 ### Bug Fixes 🐛

docs/user/codes/openmm.md

@@ -6,24 +6,17 @@
 >>> conda activate atomate2
 
 # installing atomate2
->>> pip install git+https://github.com/orionarcher/atomate2
-
-# installing classical_md dependencies
->>> conda install -c conda-forge --file .github/classical_md_requirements.txt
+>>> pip install "atomate2[openmm]"
 ```
 
 Alternatively, if you anticipate regularly updating
-atomate2 from source (which at this point, you should),
-you can clone the repository and install from source.
+atomate2 from source, you can clone the repository and install from source.
 
 ``` bash
 # installing atomate2
->>> git clone https://github.com/orionarcher/atomate2
+>>> git clone https://github.com/materialsproject/atomate2
 >>> cd atomate2
->>> git branch openff
->>> git checkout openff
->>> git pull origin openff
->>> pip install -e .
+>>> pip install -e '.[openmm]'
 ```
 
 To test the openmm installation, you can run the following command. If
@@ -458,6 +451,7 @@ run_locally(flows[rank], ensure_success=True)
 For now, you'll need to make sure you have a particular emmet branch installed.
 Later the builders will be integrated into `main`.
 
+<!-- TODO get emmet@md_builders merged -->
 ```bash
 pip install git+https://github.com/orionarcher/emmet@md_builders
 ```

docs/user/codes/vasp-workflows.csv

@@ -1,22 +1,22 @@
 Name,Type,Maker
-`Static`_,job,:obj:`.StaticMaker`
-`Relax`_,job,:obj:`.RelaxMaker`
-`Tight Relax`_,job,:obj:`.TightRelaxMaker`
-`Dielectric`_,job,:obj:`.DielectricMaker`
-`Transmuter`_,job,:obj:`.TransmuterMaker`
-`HSE06 Static`_,job,:obj:`.HSEStaticMaker`
-`HSE06 Relax`_,job,:obj:`.HSERelaxMaker`
-`HSE06 Tight Relax`_,job,:obj:`.HSETightRelaxMaker`
-`Double Relax`_,flow,:obj:`.DoubleRelaxMaker`
-`Band Structure`_,flow,:obj:`.BandStructureMaker`
-`Uniform Band Structure`_,flow,:obj:`.UniformBandStructureMaker`
-`Line-Mode Band Structure`_,flow,:obj:`.LineModeBandStructureMaker`
-`HSE06 Band Structure`_,flow,:obj:`.HSEBandStructureMaker`
-`HSE06 Uniform Band Structure`_,flow,:obj:`.HSEUniformBandStructureMaker`
-`HSE06 Line-Mode Band Structure`_,flow,:obj:`.HSELineModeBandStructureMaker`
-`Relax and Band Structure`_,flow,:obj:`.RelaxBandStructureMaker`
-`Elastic Constant`_,flow,:obj:`.ElasticMaker`
-`Optics`_,flow,:obj:`.OpticsMaker`
-`HSE06 Optics`_,flow,:obj:`.HSEOpticsMaker`
-`Phonons`_,flow,:obj:`.PhononMaker`
-`Lobster`_,flow,:obj:`.VaspLobsterMaker`
+`Static`_,job,:obj:`~atomate2.vasp.jobs.core.StaticMaker`
+`Relax`_,job,:obj:`~atomate2.vasp.jobs.core.RelaxMaker`
+`Tight Relax`_,job,:obj:`~atomate2.vasp.jobs.core.TightRelaxMaker`
+`Dielectric`_,job,:obj:`~atomate2.vasp.jobs.core.DielectricMaker`
+`Transmuter`_,job,:obj:`~atomate2.vasp.jobs.core.TransmuterMaker`
+`HSE06 Static`_,job,:obj:`~atomate2.vasp.jobs.core.HSEStaticMaker`
+`HSE06 Relax`_,job,:obj:`~atomate2.vasp.jobs.core.HSERelaxMaker`
+`HSE06 Tight Relax`_,job,:obj:`~atomate2.vasp.jobs.core.HSETightRelaxMaker`
+`Double Relax`_,flow,:obj:`~atomate2.vasp.flows.core.DoubleRelaxMaker`
+`Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.BandStructureMaker`
+`Uniform Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.UniformBandStructureMaker`
+`Line-Mode Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.LineModeBandStructureMaker`
+`HSE06 Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.HSEBandStructureMaker`
+`HSE06 Uniform Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.HSEUniformBandStructureMaker`
+`HSE06 Line-Mode Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.HSELineModeBandStructureMaker`
+`Relax and Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.RelaxBandStructureMaker`
+`Elastic Constant`_,flow,:obj:`~atomate2.vasp.flows.elastic.ElasticMaker`
+`Optics`_,flow,:obj:`~atomate2.vasp.flows.core.OpticsMaker`
+`HSE06 Optics`_,flow,:obj:`~atomate2.vasp.flows.core.HSEOpticsMaker`
+`Phonons`_,flow,:obj:`~atomate2.vasp.flows.phonons.PhononMaker`
+`Lobster`_,flow,:obj:`~atomate2.vasp.flows.lobster.VaspLobsterMaker`

docs/user/codes/vasp.md

@@ -324,7 +324,7 @@ run_locally(lobster, create_folders=True, store=SETTINGS.JOB_STORE)
 ```
 
 It is, however,  computationally very beneficial to define two different types of job scripts for the VASP and Lobster runs, as VASP and Lobster runs are parallelized differently (MPI vs. OpenMP).
-[FireWorks](https://github.com/materialsproject/fireworks) allows to run the VASP and Lobster jobs with different job scripts. Please check out the [jobflow documentation on FireWorks](https://materialsproject.github.io/jobflow/tutorials/8-fireworks.html#setting-the-manager-configs) for more information.
+[FireWorks](https://github.com/materialsproject/fireworks) allows one to run the VASP and Lobster jobs with different job scripts. Please check out the [jobflow documentation on FireWorks](https://materialsproject.github.io/jobflow/tutorials/8-fireworks.html#setting-the-manager-configs) for more information.
 
 Specifically, you might want to change the `_fworker` for the LOBSTER runs and define a separate `lobster` worker within FireWorks:
 
@@ -468,7 +468,8 @@ Finally, sometimes you have a workflow containing many VASP jobs. In this case i
 tedious to update the input sets for each job individually. Atomate2 provides helper
 functions called "powerups" that can apply settings updates to all VASP jobs in a flow.
 These powerups also contain filters for the name of the job and the maker used to
-generate them.
+generate them. These functions will apply updates *only* to VASP jobs, including those
+created dynamically - all other jobs in a flow will not be modified.
 
 ```py
 from atomate2.vasp.powerups import update_user_incar_settings

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools >= 42", "versioningit ~= 1.0", "wheel"]
+requires = ["setuptools >= 42", "versioningit >= 1,< 4", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -28,33 +28,34 @@ dependencies = [
     "PyYAML",
     "click",
     "custodian>=2024.4.18",
-    "emmet-core>=0.82.2",
+    "emmet-core>=0.84.3rc3",
     "jobflow>=0.1.11",
     "monty>=2024.7.30",
     "numpy",
     "pydantic-settings>=2.0.3",
     "pydantic>=2.0.1",
-    "pymatgen>=2024.10.3",
+    "pymatgen>=2024.11.13",
 ]
 
 [project.optional-dependencies]
 abinit = ["abipy>=0.9.3"]
 amset = ["amset>=0.4.15", "pydash"]
 cclib = ["cclib"]
 mp = ["mp-api>=0.37.5"]
-phonons = ["phonopy>=1.10.8", "seekpath"]
+phonons = ["phonopy>=1.10.8", "seekpath>=2.0.0"]
 lobster = ["ijson>=3.2.2", "lobsterpy>=0.4.0"]
 defects = [
     "dscribe>=1.2.0",
     "pymatgen-analysis-defects>=2024.5.11",
-    "python-ulid",
+    "python-ulid>=2.7",
 ]
 forcefields = [
     "ase>=3.23.0",
     "calorine<=2.2.1",
     "chgnet>=0.2.2",
     "mace-torch>=0.3.3",
     "matgl>=1.1.3",
+    "torchdata<=0.7.1",
     # quippy-ase support for py3.12 tracked in https://github.com/libAtoms/QUIP/issues/645
     "quippy-ase>=0.9.14; python_version < '3.12'",
     "sevenn>=0.9.3",
@@ -68,6 +69,7 @@ openmm = [
     "openmm-mdanalysis-reporter>=0.1.0",
     "openmm>=8.1.0",
 ]
+fireworks = ["FireWorks==2.0.3"]
 docs = [
     "FireWorks==2.0.3",
     "autodoc_pydantic==2.2.0",
@@ -84,7 +86,7 @@ dev = ["pre-commit>=2.12.1"]
 tests = [
     "FireWorks==2.0.3",
     "nbmake==1.5.4",
-    "pytest-cov==5.0.0",
+    "pytest-cov==6.0.0",
     "pytest-mock==3.14.0",
     "pytest-split==0.10.0",
     "pytest==8.3.3",
@@ -96,21 +98,21 @@ strict = [
     "click==8.1.7",
     "custodian==2024.10.16",
     "dscribe==2.1.1",
-    "emmet-core==0.84.2",
+    "emmet-core==0.84.3rc3",
     "ijson==3.3.0",
     "jobflow==0.1.18",
     "lobsterpy==0.5.0",
     "mdanalysis==2.7.0",
-    "monty==2024.7.30",
+    "monty==2024.10.21",
     "mp-api==0.42.2",
     "numpy",
     "openmm-mdanalysis-reporter==0.1.0",
     "openmm==8.1.1",
     "phonopy==2.27.0",
-    "pydantic-settings==2.6.0",
+    "pydantic-settings==2.6.1",
     "pydantic==2.9.2",
-    "pymatgen-analysis-defects==2024.7.19",
-    "pymatgen==2024.10.3",
+    "pymatgen-analysis-defects==2024.10.22",
+    "pymatgen==2024.11.13",
     "python-ulid==3.0.0",
     "seekpath==2.1.0",
     "tblite==0.3.0; python_version < '3.12'",
@@ -119,11 +121,11 @@ strict = [
 strict-forcefields = [
     "calorine==3.0",
     "chgnet==0.4.0",
-    "mace-torch>=0.3.3",
+    "mace-torch>=0.3.6",
     "matgl==1.1.3",
     "quippy-ase==0.9.14; python_version < '3.12'",
-    "sevenn==0.10.0",
-    "torch==2.5.0",
+    "sevenn==0.10.1",
+    "torch==2.5.1",
     "torchdata==0.7.1",                            # TODO: remove when issue fixed
 ]
 

src/atomate2/ase/jobs.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import logging
+from abc import ABCMeta, abstractmethod
 from dataclasses import dataclass, field
 from typing import TYPE_CHECKING
 
@@ -28,7 +29,7 @@
 
 
 @dataclass
-class AseMaker(Maker):
+class AseMaker(Maker, metaclass=ABCMeta):
     """
     Define basic template of ASE-based jobs.
 
@@ -44,8 +45,6 @@ class AseMaker(Maker):
         The name of the job
     calculator_kwargs : dict
         Keyword arguments that will get passed to the ASE calculator.
-    calculator_kwargs : dict
-        Keyword arguments that will get passed to the ASE calculator.
     ionic_step_data : tuple[str,...] or None
         Quantities to store in the TaskDocument ionic_steps.
         Possible options are "struct_or_mol", "energy",
@@ -70,6 +69,7 @@ class AseMaker(Maker):
     store_trajectory: StoreTrajectoryOption = StoreTrajectoryOption.NO
     tags: list[str] | None = None
 
+    @abstractmethod
     def run_ase(
         self,
         mol_or_struct: Structure | Molecule,
@@ -92,6 +92,7 @@ def run_ase(
         raise NotImplementedError
 
     @property
+    @abstractmethod
     def calculator(self) -> Calculator:
         """ASE calculator, method to be implemented in subclasses."""
         raise NotImplementedError

src/atomate2/ase/md.py

@@ -7,6 +7,7 @@
 import os
 import sys
 import time
+from abc import ABCMeta, abstractmethod
 from collections.abc import Sequence
 from dataclasses import dataclass, field
 from enum import Enum
@@ -78,7 +79,7 @@ class DynamicsPresets(Enum):
 
 
 @dataclass
-class AseMDMaker(AseMaker):
+class AseMDMaker(AseMaker, metaclass=ABCMeta):
     """
     Perform MD with the Atomic Simulation Environment (ASE).
 
@@ -393,6 +394,7 @@ def _callback(dyn: MolecularDynamics = md_runner) -> None:
         )
 
     @property
+    @abstractmethod
     def calculator(self) -> Calculator:
         """ASE calculator, to be overwritten by user."""
         raise NotImplementedError